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Question: DEXseq ignoreRank
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gravatar for Marco Marconi
3.6 years ago by
Marco Marconi40 wrote:
Hello, i get this strange error: dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= ~ sample + exon + condition:exon,flattenedfile=flattenedFile ) Error in DESeqDataSet(se, design, ignoreRank = TRUE) : unused argument (ignoreRank = TRUE) it seems to be an internal error of the DEXSeqDataSetFromHTSeq function, I couldn't find any workaround.... thanks [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.6 years ago by Michael Love15k • written 3.6 years ago by Marco Marconi40
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gravatar for Michael Love
3.6 years ago by
Michael Love15k
United States
Michael Love15k wrote:
hi Marco, Always paste the output of sessionInfo(), as it helps maintainers diagnose the problem. I would guess you are using a release version of DEXSeq, but DESeq2 version < 1.4? Mike On Mon, May 12, 2014 at 9:35 AM, Marco Marconi <marco.marconi@gmail.com>wrote: > Hello, i get this strange error: > > dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= ~ > sample + exon + condition:exon,flattenedfile=flattenedFile ) > > Error in DESeqDataSet(se, design, ignoreRank = TRUE) : > unused argument (ignoreRank = TRUE) > > > it seems to be an internal error of the DEXSeqDataSetFromHTSeq function, I > couldn't find any workaround.... > > thanks > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 3.6 years ago by Michael Love15k
mmm....have a look :P > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DEXSeq_1.10.3 BiocParallel_0.6.0 DESeq2_1.4.4 [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1 GenomicRanges_1.16.3 [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Biobase_2.24.0 [10] BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] annotate_1.42.0 AnnotationDbi_1.26.0 BatchJobs_1.2 [4] BBmisc_1.6 biomaRt_2.20.0 Biostrings_2.32.0 [7] bitops_1.0-6 brew_1.0-6 codetools_0.2-8 [10] DBI_0.2-7 digest_0.6.4 fail_1.2 [13] foreach_1.4.2 genefilter_1.46.1 geneplotter_1.42.0 [16] grid_3.1.0 hwriter_1.3 iterators_1.0.7 [19] lattice_0.20-29 locfit_1.5-9.1 plyr_1.8.1 [22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.16.0 [25] RSQLite_0.11.4 sendmailR_1.1-2 splines_3.1.0 [28] statmod_1.4.19 stats4_3.1.0 stringr_0.6.2 [31] survival_2.37-7 tools_3.1.0 XML_3.98-1.1 [34] xtable_1.7-3 XVector_0.4.0 zlibbioc_1.10.0 On 12 May 2014 15:49, Michael Love <michaelisaiahlove@gmail.com> wrote: > hi Marco, > > Always paste the output of sessionInfo(), as it helps maintainers diagnose > the problem. > > I would guess you are using a release version of DEXSeq, but DESeq2 > version < 1.4? > > Mike > > > On Mon, May 12, 2014 at 9:35 AM, Marco Marconi <marco.marconi@gmail.com>wrote: > >> Hello, i get this strange error: >> >> dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= ~ >> sample + exon + condition:exon,flattenedfile=flattenedFile ) >> >> Error in DESeqDataSet(se, design, ignoreRank = TRUE) : >> unused argument (ignoreRank = TRUE) >> >> >> it seems to be an internal error of the DEXSeqDataSetFromHTSeq function, I >> couldn't find any workaround.... >> >> thanks >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 3.6 years ago by Marco Marconi40
Fair enough. Could you try reinstalling DESeq2? The error is R reporting that this function doesn't have an argument which it should have in v1.4. Mike On Mon, May 12, 2014 at 9:51 AM, Marco Marconi <marco.marconi at="" gmail.com=""> wrote: > > mmm....have a look :P > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] DEXSeq_1.10.3 BiocParallel_0.6.0 DESeq2_1.4.4 > [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1 GenomicRanges_1.16.3 > [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Biobase_2.24.0 > [10] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] annotate_1.42.0 AnnotationDbi_1.26.0 BatchJobs_1.2 > [4] BBmisc_1.6 biomaRt_2.20.0 Biostrings_2.32.0 > [7] bitops_1.0-6 brew_1.0-6 codetools_0.2-8 > [10] DBI_0.2-7 digest_0.6.4 fail_1.2 > [13] foreach_1.4.2 genefilter_1.46.1 geneplotter_1.42.0 > [16] grid_3.1.0 hwriter_1.3 iterators_1.0.7 > [19] lattice_0.20-29 locfit_1.5-9.1 plyr_1.8.1 > [22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.16.0 > [25] RSQLite_0.11.4 sendmailR_1.1-2 splines_3.1.0 > [28] statmod_1.4.19 stats4_3.1.0 stringr_0.6.2 > [31] survival_2.37-7 tools_3.1.0 XML_3.98-1.1 > [34] xtable_1.7-3 XVector_0.4.0 zlibbioc_1.10.0 > > > > On 12 May 2014 15:49, Michael Love <michaelisaiahlove at="" gmail.com=""> wrote: >> >> hi Marco, >> >> Always paste the output of sessionInfo(), as it helps maintainers diagnose the problem. >> >> I would guess you are using a release version of DEXSeq, but DESeq2 version < 1.4? >> >> Mike >> >> >> On Mon, May 12, 2014 at 9:35 AM, Marco Marconi <marco.marconi at="" gmail.com=""> wrote: >>> >>> Hello, i get this strange error: >>> >>> dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= ~ >>> sample + exon + condition:exon,flattenedfile=flattenedFile ) >>> >>> Error in DESeqDataSet(se, design, ignoreRank = TRUE) : >>> unused argument (ignoreRank = TRUE) >>> >>> >>> it seems to be an internal error of the DEXSeqDataSetFromHTSeq function, I >>> couldn't find any workaround.... >>> >>> thanks >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >
ADD REPLYlink written 3.6 years ago by Michael Love15k
works fine now, thanks On 12 May 2014 16:03, Michael Love <michaelisaiahlove@gmail.com> wrote: > Fair enough. > > Could you try reinstalling DESeq2? The error is R reporting that this > function doesn't have an argument which it should have in v1.4. > > Mike > > > On Mon, May 12, 2014 at 9:51 AM, Marco Marconi <marco.marconi@gmail.com> > wrote: > > > > mmm....have a look :P > > > > > sessionInfo() > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] DEXSeq_1.10.3 BiocParallel_0.6.0 DESeq2_1.4.4 > > [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1 GenomicRanges_1.16.3 > > [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Biobase_2.24.0 > > [10] BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.42.0 AnnotationDbi_1.26.0 BatchJobs_1.2 > > [4] BBmisc_1.6 biomaRt_2.20.0 Biostrings_2.32.0 > > [7] bitops_1.0-6 brew_1.0-6 codetools_0.2-8 > > [10] DBI_0.2-7 digest_0.6.4 fail_1.2 > > [13] foreach_1.4.2 genefilter_1.46.1 geneplotter_1.42.0 > > [16] grid_3.1.0 hwriter_1.3 iterators_1.0.7 > > [19] lattice_0.20-29 locfit_1.5-9.1 plyr_1.8.1 > > [22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.16.0 > > [25] RSQLite_0.11.4 sendmailR_1.1-2 splines_3.1.0 > > [28] statmod_1.4.19 stats4_3.1.0 stringr_0.6.2 > > [31] survival_2.37-7 tools_3.1.0 XML_3.98-1.1 > > [34] xtable_1.7-3 XVector_0.4.0 zlibbioc_1.10.0 > > > > > > > > On 12 May 2014 15:49, Michael Love <michaelisaiahlove@gmail.com> wrote: > >> > >> hi Marco, > >> > >> Always paste the output of sessionInfo(), as it helps maintainers > diagnose the problem. > >> > >> I would guess you are using a release version of DEXSeq, but DESeq2 > version < 1.4? > >> > >> Mike > >> > >> > >> On Mon, May 12, 2014 at 9:35 AM, Marco Marconi <marco.marconi@gmail.com> > wrote: > >>> > >>> Hello, i get this strange error: > >>> > >>> dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= > ~ > >>> sample + exon + condition:exon,flattenedfile=flattenedFile ) > >>> > >>> Error in DESeqDataSet(se, design, ignoreRank = TRUE) : > >>> unused argument (ignoreRank = TRUE) > >>> > >>> > >>> it seems to be an internal error of the DEXSeqDataSetFromHTSeq > function, I > >>> couldn't find any workaround.... > >>> > >>> thanks > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > > > [[alternative HTML version deleted]]
ADD REPLYlink written 3.6 years ago by Marco Marconi40
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